TABLE 3.

The list of detected QTLs for 660 nm using different GWAS methods in the tested soybean panel.

GWAS Method	Chromosome	Peak SNP position	Co-located QTL	Environmenta	References
MLM	3	22283184		NA
		22283218		NA
		22283256		NA
		44326068		NA
	7	20220381		NA
		20280812		NA
		23349322		NA
	18	56952847	pod number 4-g8	NA	Hao et al., 2012
			plant height 3-g14	NA	Contreras-Soto et al., 2017
		56952858	shoot K 1-g39	NA	Dhanapal et al., 2018
			WUE 3-g32	NA	Dhanapal et al., 2018
FarmCPU	3	22283184		NA
		22283218		NA
		22283256		NA
		44326068		NA
	7	20220330	Shoot Mn 1-g2	NA	Dhanapal et al., 2018
		20220381		NA
		20280812		NA
		23317163	Ureide content 1-g9	NA	Ray et al., 2015
		23349322	shoot Mn 1-g3	NA	Dhanapal et al., 2018
		27492738		NA
	18	56952847	pod number 4-g8	NA	Hao et al., 2012
			plant height 3-g14	NA	Contreras-Soto et al., 2017
		56952858	shoot K 1-g39	NA	Dhanapal et al., 2018
			WUE 3-g32	NA	Dhanapal et al., 2018
		57794992		NA
SVR	14	16425108		NA
	15	13118545		NA
		12895268		NA
		12894320		NA
		14174744		NA
		14378690		1
		12892003	seed coat color 3-g3	NA	Vuong et al., 2015
			seed yield, soyNAM 7-g14	NA	Diers et al., 2018
		18302021		NA
		14406716		1
		17877705		NA
		17362699		NA
		14088239		1
		13163194	SCN 5-g33	NA	Li et al., 2016
			First flower 4-g58	NA	Mao et al., 2017
			First Flower 5-g29.1	NA	Fang et al., 2017
			First flower 5-g29.2	NA	Fang et al., 2017
			First flower 5-g29.3	NA	Fang et al., 2017
		14421366		1
	19	36064225		1

^aDetected in separate environments in addition to the combined environment. (1) 2018Ridgetown, (2) 2019Ridgetwon, (3) 2018Palmyra, (4) 2019Palmyra, (NA) not found in any separate environment.

MLM, mixed linear model; FarmCPU, fixed and random model circulating probability unification; RF, random forest; SVR, support vector regression.